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Bioinformatics Advance Access originally published online on May 28, 2008
Bioinformatics 2008 24(14):1625-1631; doi:10.1093/bioinformatics/btn249
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

InteroPORC: automated inference of highly conserved protein interaction networks

Magali Michaut 1,2,*, Samuel Kerrien 2, Luisa Montecchi-Palazzi 2, Franck Chauvat 1, Corinne Cassier-Chauvat 1,3, Jean-Christophe Aude 1, Pierre Legrain 1 and Henning Hermjakob 2

1CEA, IBITECS, Gif sur Yvette, F-91191, France, 2EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and 3CNRS, URA 2096, Gif sur Yvette, F-91191, France

*To whom correspondence should be addressed.


  Abstract

Motivation: Protein–protein interaction networks provide insights into the relationships between the proteins of an organism thereby contributing to a better understanding of cellular processes. Nevertheless, large-scale interaction networks are available for only a few model organisms. Thus, interologs are useful for a systematic transfer of protein interaction networks between organisms. However, no standard tool is available so far for that purpose.

Results: In this study, we present an automated prediction tool developed for all sequenced genomes available in Integr8. We also have developed a second method to predict protein–protein interactions in the widely used cyanobacterium Synechocystis. Using these methods, we have constructed a new network of 8783 inferred interactions for Synechocystis.

Availability: InteroPORC is open-source, downloadable and usable through a web interface at http://biodev.extra.cea.fr/interoporc/

Contact: michaut.bioinfo{at}gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Burkhard Rost

Received on February 18, 2008; revised on May 26, 2008; accepted on May 26, 2008

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